Skip to content

Instantly share code, notes, and snippets.

View oeway's full-sized avatar

Wei Ouyang oeway

  • Science For Life Laboratory
  • Stockholm
View GitHub Profile
<config lang="json">
{
"name": "BIO-RDF-Validator",
"type": "web-python",
"version": "0.1.0",
"description": "A spec validator for bioimage RDF files.",
"tags": [],
"ui": "",
"cover": "",
"inputs": null,
import micropip
await micropip.install('pyotritonclient')
import io
from PIL import Image
import matplotlib.pyplot as plt
import numpy as np
from js import fetch
from pyotritonclient import get_config, execute_model
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "HPASingleCellTriton",
"type": "web-python",
"version": "0.1.0",
"description": "[TODO: describe this plugin with one sentence.]",
@oeway
oeway / convert_hpa_image_jimp.js
Created September 21, 2021 18:20
Read HPA images with jimp
import {InferenceSession, Tensor} from 'onnxruntime-web';
import Jimp from 'jimp/es';
const COLORS = ["red", "green", "blue", "yellow"]
async function handleRun(e) {
e.preventDefault();
// create an inference session, using WebGL backend. (default is 'wasm')
const baseURL = 'https://images.proteinatlas.org/115/672_E2_1_'
const imgTensor = new Float32Array(1024*1024*4)
@oeway
oeway / PythonPlugin.imjoy.html
Last active June 30, 2023 01:30
Read image file with Pyodide in ImJoy
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "PythonPlugin",
"type": "web-python",
"version": "0.1.0",
"description": "[TODO: describe this plugin with one sentence.]",
<docs lang="markdown">
## PyImageJ demo
A PyImageJ demo ported from https://github.com/imagej/pyimagej
</docs>
<config lang="json">
{
"name": "N2V-Fiji-Demo",
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "DownloadFileWebPython",
"type": "web-python",
"version": "0.1.0",
"description": "[TODO: describe this plugin with one sentence.]",

ImageJ.JS: ImageJ in the browser

Wei OUYANG

Emma Lundberg Group @ KTH Royal Institute of Technology


ImageJ.JS

  • ImageJ compiled into Javascript (with CheerpJ)
  • Running in web browser, support tablets & mobile phones
<docs>
# HPA Cell Atlas Images
This plugin uses the virtual stack api of ImageJ.JS to display all the HPA Cell Atlas images (v18).
</docs>
<config lang="json">
{
"name": "HPACellAtlasImages",
"type": "iframe",
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.